[Cypher]

You can delete the "Omnifocus.ofocus" file stored in the ~/Library/Application Support/OmniFocus/ folder

Close Omnifocus and turn off syncing if you use it. Then I would copy the omnifocus file to a backup location just incase you decide to re-use it. Then delete the original omnifocus.ofocus file from the library.

Once you restart omnifocus, it should then recreate a new blank database.